These supplementary data contain input and output files of EMTO density-functional theory (DFT) calculations and IPython/Jupyter notebooks that were used in analyzing the data for the paper "Challenges in automated high-throughput ab initio thermodynamics of magnetic high-entropy alloys". The data are organized as follows: alloy_discovery folder contains the analysis notebooks and the processed EMTO DFT output data in a h5 database. An installation of Python and Jupyter notebooks is required to run the notebooks. A recommended way of installing them is the Anaconda Python distribution: https://www.anaconda.com/download/ It is recommended to first run the Requirements notebook, which checks what Python dependencies are needed to be downloaded. DFT output data is stored as an HDF5 database is located in the results subfolder. Figures generated with the notebooks are located in the output_figures subfolder. output_files folder contains raw output files of EMTO DFT calculations. input_files folder contains raw input files that were used in the EMTO DFT calculations.